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benjjneb / dada2

Accurate sample inference from amplicon data with single nucleotide resolution
http://benjjneb.github.io/dada2/
GNU Lesser General Public License v3.0
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dsrA amplicon analisys with DADA2 #421

Closed DanielC-G closed 6 years ago

DanielC-G commented 6 years ago

Dear benjjneb. I used DADA2 to process amplicons of dsrA genes, but I am not sure if DADA2 is suitable for it. The preliminary results look good but I want to take advise from you about to use DADA2 for different marker genes.

Regards.

joey711 commented 6 years ago

There is nothing about DADA2 (the algorithm) implemented in dada2 (the package) that is specific to the gene target. The dada2 package does include some support for tasks that are 16S-specific, but these are independent downstream convenience functions, and are in no way required.

The best way to convince yourself is to sequence a control sample(s) where you know the correct answer(s) for the exact sequence(s), and evaluate how well dada2 did in returning the correct result.

DanielC-G commented 6 years ago

Thank you for you replay joey711, I will consider your advice.

zinuska commented 5 years ago

Hello,

I have a project where I have paralelly sequenced 16S and functional gene (bssA - for anaerobic toluene degradation) amplicons in various microbial communities. I am developing a workflow to analyze my data. So far I had a mixed workflow combining mothur (to correct the mixed orientation) and qiime1. As I understand, DADA2 would be a much better option for me in combination with SMRTLink. Before I go deeper into DADA2, I want to ask some questions:

My bssA in-house database has been created in ARB and contains aligned sequences of very different formats: some full operons, and many sequences of the alpha-subunit of my gene (what I actually target myself), where many amplicon sequences were obtained with different primers. Therefore, it was my PIs decision to not cut the primers off of the sequences (for traceability and whatsoever). This would disqualify my data for DADA2 as I understand. Is there still a way to overcome this issue? If I remove the primers from my current dataset, than assigning taxonomy using my in-house database would not give an exact match for sure.

Regards, Anna

vfonti commented 3 years ago

@DanielC-G I am considering to do something similar. How have you prepared the libraries and sequenced them?

DanielC-G commented 3 years ago

@vfonti We used the protocol of this paper https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.13139, but using dada2: https://link.springer.com/article/10.1007%2Fs00248-020-01631-5